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- PDB-3a1p: Structure of Ribosome maturation protein RimM and Ribosomal prote... -

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Basic information

Entry
Database: PDB / ID: 3a1p
TitleStructure of Ribosome maturation protein RimM and Ribosomal protein S19
Components
  • 30S ribosomal protein S19
  • Ribosome maturation factor rimM
KeywordsRIBOSOMAL PROTEIN / RimM N-terminal domain / PRC-barrel domain / beta barrels / ribosome / 30S ribosomal subunit / ribosome biogenesis / 16S rRNA processing / rRNA binding / protein-protein complex / Chaperone / Cytoplasm / Ribonucleoprotein / RNA-binding / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


rRNA processing / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / cytosolic small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / cytoplasm
Similarity search - Function
RimM / PRC-barrel domain / RimM, N-terminal / 16S rRNA processing protein RimM / RimM, N-terminal domain superfamily / RimM N-terminal domain / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / PRC-barrel domain / PRC-barrel domain ...RimM / PRC-barrel domain / RimM, N-terminal / 16S rRNA processing protein RimM / RimM, N-terminal domain superfamily / RimM N-terminal domain / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / PRC-barrel domain / PRC-barrel domain / PRC-barrel-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 / Ribosomal protein S19, bacterial-type / SH3 type barrels. / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Translation protein, beta-barrel domain superfamily / Roll / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein uS19 / Ribosome maturation factor RimM
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsKaminishi, T. / Takemoto, C. / Tatsuguchi, A. / Kawazoe, M. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structure of Ribosome maturation protein RimM and Ribosomal protein S19
Authors: Kaminishi, T. / Takemoto, C. / Tatsuguchi, A. / Kawazoe, M. / Shirouzu, M. / Yokoyama, S.
History
DepositionApr 21, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome maturation factor rimM
B: 30S ribosomal protein S19
C: Ribosome maturation factor rimM
D: 30S ribosomal protein S19


Theoretical massNumber of molelcules
Total (without water)57,4005
Polymers57,4004
Non-polymers01
Water7,314406
1
A: Ribosome maturation factor rimM
B: 30S ribosomal protein S19


Theoretical massNumber of molelcules
Total (without water)28,7002
Polymers28,7002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-16 kcal/mol
Surface area12590 Å2
MethodPISA
2
C: Ribosome maturation factor rimM
D: 30S ribosomal protein S19


Theoretical massNumber of molelcules
Total (without water)28,7003
Polymers28,7002
Non-polymers01
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-16 kcal/mol
Surface area13310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.397, 67.491, 62.002
Angle α, β, γ (deg.)90.000, 94.820, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribosome maturation factor rimM


Mass: 18094.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: rimM / Plasmid: pET-11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJH5
#2: Protein 30S ribosomal protein S19


Mass: 10605.464 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: rpsS / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHP2
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M sodium cacodylate, 0.2M sodium acetate trihydrate, 30%[w/v] polyethylene glycol 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2006
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, direct water cooling using micro-channel (1st crystal), indirect water cooling (2nd crystal).
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20948 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.108 / Χ2: 1.095 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 2079 / Rsym value: 0.654 / Χ2: 0.958 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO / Packing: 0
Highest resolutionLowest resolution
Rotation2.51 Å45.57 Å
Translation2.51 Å45.57 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1.2refinement
PDB_EXTRACT3.004data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DYI AND 2E5L FOR RIMM AND RIBOSOMAL PROTEIN S19, RESPECTIVELY.

2dyi

2e5l


Resolution: 2.3→45.57 Å / Rfactor Rfree error: 0.007 / FOM work R set: 0.822 / Data cutoff high absF: 1024030.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1076 5.1 %RANDOM
Rwork0.197 ---
obs-20934 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.407 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-3.32 Å2
2--2.05 Å20 Å2
3----1.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 1 406 4317
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.591.5
X-RAY DIFFRACTIONc_mcangle_it2.72
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it3.312.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.331 105 5.5 %
Rwork0.27 1801 -
all-1906 -
obs--91.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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